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Abstract

HIV-1 is a rapidly evolving virus that has infected tens of millions of individuals throughout the world. Studies on HIV-1 are described various aspects of viral evolution, however, many questions concerning the evolution of HIV-1 remain unanswered. It has been hypothesized that viruses of, subtype E, found in Thailand and in the Central African Republic, are derived from a recombinant lineage. Using several phylogenetic, statistical, and simulation analyses, we show that there is inadequate support for this recombinant hypothesis and that the subtype E variants are most likely a separate monophyletic group.Other analyses focus on a group of 100 individuals from the United States who are all infected with subtype B viruses. These studies focus on the evolution of viruses both within and between various groups of individuals. Using this set of sequences, we were able to create a new model of sequence evolution, through implementing a technique that estimated maximum likelihood substitution rates from a previously constructed phylogenetic topology. We were also able to correlate patterns of genetic diversity with epidemiological information, including risk and demographic factors, using the techniques of phylogenetic tree construction, phenetic tree construction, and multidimensional scaling. Furthermore, we were able to predict group membership for several risk and demographic factors using tree construction techniques and discriminant functions analyses. The ability to identify subtle phylogenetic structures and predict risk factors and demographic group designations in sequences that contain little signal is an important step in better understanding the evolution and dynamics of the HIV-1 pandemic.